Contacts of the helix formed by residues 1247 - 1255 (chain D) in PDB entry 5UHE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1247 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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883D ASP* 4.0 10.5 - - - -
1246D ASN* 1.3 76.9 - - - +
1248D LEU* 1.3 65.9 + - - -
1249D LYS 3.5 1.6 - - - -
1250D GLU* 3.3 21.0 + - - -
1251D ASN* 2.3 37.9 + - - +
1259D PRO* 3.6 9.1 - - - +
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Residues in contact with LEU1248 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1077C GLN* 3.4 13.2 - - + +
882D GLN* 3.2 40.8 + - + +
883D ASP* 4.6 2.8 + - - -
885D ILE* 4.0 12.6 - - + -
994D ALA* 4.7 1.3 - - + -
997D ILE* 3.5 30.5 - - + -
1247D GLY* 1.3 70.2 - - - +
1249D LYS* 1.3 66.9 + - - +
1250D GLU* 4.1 0.2 + - - -
1251D ASN* 3.3 2.4 + - - +
1252D VAL* 3.1 30.5 + - - +
1258D ILE* 3.6 30.4 - - + +
1259D PRO* 4.1 11.9 - - + +
1260D ALA* 3.8 21.1 - - + -
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Residues in contact with LYS1249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C GLU* 4.1 7.9 + - - -
1074C TRP* 4.9 8.5 - - - +
1077C GLN* 6.0 0.2 - - - +
418D LEU* 3.6 37.9 - - + +
875D ARG* 4.6 3.6 + - - +
878D VAL* 5.1 2.4 - - - +
879D ASP* 3.2 36.6 + - - +
882D GLN* 3.1 29.3 + - - +
1222D SER* 3.4 14.1 - - - +
1225D SER* 3.4 33.0 - - - +
1226D PHE* 4.5 2.2 - - - +
1248D LEU* 1.3 80.0 - - - +
1250D GLU* 1.3 72.0 + - - +
1251D ASN 3.2 0.7 + - - -
1252D VAL* 3.3 5.8 + - - +
1253D ILE* 3.2 29.0 + - + +
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Residues in contact with GLU1250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882D GLN* 4.4 1.9 - - - +
883D ASP* 4.5 6.6 - - - +
1217D THR* 5.3 0.9 + - - -
1218D ASP* 4.6 7.1 - - - +
1219D SER* 3.1 39.2 - - - +
1221D LEU* 3.9 18.1 - - + +
1222D SER* 3.5 8.2 + - - -
1243D ASP* 3.8 9.2 - - - +
1244D LYS 5.2 0.9 - - - +
1245D LEU* 4.4 11.7 - - + -
1246D ASN 4.1 6.2 + - - +
1247D GLY* 3.3 31.3 + - - +
1248D LEU 4.1 0.2 + - - -
1249D LYS* 1.3 92.1 + - - +
1251D ASN* 1.3 61.6 + - - +
1253D ILE* 3.6 4.0 + - - +
1254D ILE* 3.2 26.4 + - - +
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Residues in contact with ASN1251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245D LEU 3.7 11.8 + - - -
1246D ASN* 4.0 0.2 - - - +
1247D GLY 2.3 47.8 + - - +
1248D LEU 3.9 2.2 - - - +
1249D LYS 3.2 0.2 - - - -
1250D GLU* 1.3 73.9 - - - +
1252D VAL* 1.3 59.1 + - - +
1253D ILE 3.1 1.6 - - - -
1254D ILE* 3.7 7.0 - - - -
1255D GLY 2.8 31.5 + - - -
1256D LYS* 3.1 57.5 + - - +
1257D LEU 3.3 5.2 - - - +
1258D ILE* 4.1 4.0 - - - -
1259D PRO* 3.5 20.7 - - + +
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Residues in contact with VAL1252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073C CYS* 4.6 5.4 - - - -
1077C GLN* 4.0 15.7 - - - +
1085C LEU* 4.0 17.0 - - + -
1089C LEU* 3.7 29.3 - - + +
1118C PRO* 5.6 0.3 - - - +
417D LEU 3.7 13.9 - - - +
418D LEU* 4.3 15.7 - - + -
420D LYS* 4.4 6.9 + - - -
1248D LEU 3.1 21.3 + - - +
1249D LYS* 3.8 5.8 - - - +
1251D ASN* 1.3 77.2 - - - +
1253D ILE* 1.3 63.6 + - - +
1255D GLY* 3.7 6.5 + - - -
1256D LYS 4.8 1.8 - - - -
1258D ILE* 3.8 19.5 - - + -
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Residues in contact with ILE1253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118C PRO* 4.0 12.0 - - - +
1121C PHE* 3.4 33.4 - - + +
1124C LEU* 5.0 0.2 - - + -
413D PHE* 4.7 7.6 - - + -
417D LEU* 3.8 38.3 - - + +
418D LEU* 4.5 13.7 - - + -
420D LYS* 4.7 1.4 + - - -
1221D LEU* 3.7 31.4 - - + +
1225D SER* 4.3 24.7 - - - +
1249D LYS 3.2 17.7 - - - +
1250D GLU 3.6 7.2 - - - +
1251D ASN 3.1 0.4 - - - -
1252D VAL* 1.3 80.5 - - - +
1254D ILE* 1.3 60.6 + - - +
1255D GLY 3.5 0.2 + - - -
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Residues in contact with ILE1254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C ILE* 4.6 4.7 - - - +
1118C PRO* 3.1 21.2 - - - +
1121C PHE* 3.6 37.9 - - + -
5D ASN* 4.6 7.4 + - - +
7D PHE* 4.9 14.8 - - + -
10D LEU* 5.1 0.2 - - + -
1221D LEU* 4.5 7.0 - - + -
1245D LEU* 3.7 43.3 - - + -
1250D GLU 3.2 18.8 - - - +
1251D ASN* 3.3 10.1 - - - +
1253D ILE* 1.3 76.0 - - - +
1255D GLY* 1.3 61.5 + - - +
1256D LYS* 3.8 27.1 - - + +
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Residues in contact with GLY1255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086C GLN* 3.3 24.2 + - - +
1090C THR* 4.4 14.4 - - - +
1116C GLY 4.8 1.0 - - - +
1118C PRO* 4.2 11.4 - - - -
5D ASN* 3.7 15.1 + - - +
1251D ASN 2.8 11.6 + - - -
1252D VAL* 3.7 5.4 + - - -
1253D ILE 3.3 2.6 - - - -
1254D ILE* 1.3 75.9 - - - +
1256D LYS* 1.3 62.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il